Skipper's Secret
by BookWriter2014
Summary: It has been six years since Private joined the team, but now a ghost from the young penguin's past has returned and soon Private learns that everyone has secrets, even his own team. Unfortunately, Skipper's best kept secret may not only turn Private against him, but tear his whole world apart. Sequel to Skipper's Enemy.
1. Chapter 1

Chapter One

"You guys ready for the big game?" Marlene asked as she hopped down into their HQ.

Skipper spun around, his blue and gold helmet almost falling off, his eyes narrowed, and flippers raised; ready to fight. "Hoover Damn, Marlene. Knock before you enter. I could have taken you out if you'd been one step closer."

Private smiled and shook his head, he'd long since gotten used to his leader's paranoia, as well as his readiness to fight at a minute's notice. Even on Game day.

"Yeah, I know, you're being paranoid, Skipper," Marlene rolled her eyes and walked over to them, the side of her face painted with the team's colors.

"Hey Private," she said as she passed him.

"Hey Marlene," Private replied, while Marlene stopped in front of Skipper, placing her paws on her hips.

"So whose ready for game day?' she asked cheerfully, glancing past Skipper at the TV, now turned onto the sports channel, with Rico glued to it, crunching down on the snacks for the game.

"Oh I know I am," Skipper said as if he hadn't just about attacked her; relaxing his posture, "I've got my fangear on, and the snacks are all ready—"

"Noe," Rico burped, and Private saw that he had eaten all of the snacks.

"Oh, Rico," Skipper glared angrily at the other penguin, flippers crossed across his chest in annoyance. Marlene stood beside him.

"I can go get them if you want Skipper," Private volunteered, after all he wouldn't see the game. It was nothing like actual football, which the others referred to as Soccer. Private didn't see the point in throwing around a misshapen ball for a couple of hours, though everyone else seemed to enjoy it. Except for the chimps that was.

"But you'll miss the game," Marlene said, sounding confused.

"He doesn't watch actual football," Skipper sighed, rolling his eyes. The older penguin tossed the bowl at him, "Just be sure to take Kowalski with you. I don't want him blowing anything up—"

Suddenly the channel changed, and Chuck Charles, the news anchor was on, talking about some insedent involving the animal control HQ in which some of the animals had escaped.

"Wait, is that Savio?" Private stared at the tv as it showed a big yellow boa, exactly like Savio, the snake who had tried to eat multiply zoo animals before being shipped elsewhere, "I thought he was still in Hoboken".

"Kowalski get out here," Skipper said, his expression unreadable.

Kowalski stepped out of the lab, annoyed, "What, I was this close to solving Pi to—is that Savio?" he stopped beside Rico, and stared at the tv.

According to Chuck Charles, he had last been seen swimming in the bay.

Skipper's voice drew Private's attention back to his leader, who was still standing beside Marlene, "Look's like we've got ourselves a new mission boys, let's go!"

 _I hope you guys will enjoy this new story. Sorry about the wait in getting it up._


	2. Chapter 2

Chapter Two

"So where is the snake guy?" Julian asked as they turned a corner in the city. The lemur king had insisted on coming with them to face the giant snake after he had overheard them talking about it as they left. Or moreover when Marlene had been going back to her habitat, telling them good luck on their mission.

"Be quiet Ringtail, we're working on it," Skipper muttered angrily from where he was leading the group and talking with Kowalski about the possibilities of where the snake could be by now.

"He's probably somewhere near the harbor; so if I'm correct, which I usually am, we should be encountering him soon," Kowalski said flipping through his notepad.

"Alright boys, keep a watchful eye out," Skipper said. Private nodded, and fell into position; he had been assigned to protect Julian in case the lemur got cold feet at the last minute.

They moved forward silently, ready to attack, when suddenly a voice behind them spoke.

"Why hello Soon to be ex: King Julian," they all spun around to see an orange and black lemur with green eyes standing smugly behind them.

"Clemson!" Julian glared at the lemur in fury, "I thought this guy was locked up in the Hoboken?" Private silently agreed with Julian, the last time they had seen the lemur had been when they had created an uneasy alliance with him and several other villians in order to defeat a crazy zookeeper who hated animals.

"How'd you get out!" Kowalski asked in envy.

"Kowalski, less talking, more punching," Skipper rolled his eyes and leapt forward, easily pinning Clemson to the ground, "Who cares how he got out, what's important is that we're taking him back".

"Are you sure you can take all of us back?" Savio purred from where he was slithering out of the harbor sea.

"All of us?" Private echoed, feeling a twinge of fear in his gut.

"All of us," a deep muscular voice said, and suddenly King rat lifted the sewer grate and his minions began pouring out of the sewer, surrounding them.

"Boys, fight for all you're worth!" Skipper yelled, and instantly the harbor exploded into battle.

Private punched and kicked every rat he could, though he lost track of where Julian had tackled Clemson after Skipper had taken on the Rat King.

Suddenly, he felt Savio's coils curl around him, and he was unable to move, despite how much he wriggled and twisted to try and get himself free.

"Skipper!" he yelled, hoping his leader would hear him.

Skipper ducked around Rat King and turned his head, his sapphire eyes widening in shock at seeing Private in danger, "Private! Hang on!" he yelled and began to belly slide through the crowd towards him.

"Stop squirming so much, there's someone who wants to meet you," Savio hissed, and began to slither away, Private still in his coils.

Private turned his head to see the rest of his team, along with Julian being overpowered by their enemies, it seemed that King Rat's army had tripled in size.

 _Hope you guys enjoyed this chapter._


	3. Chapter 3

Chapter Three

Savio dragged Private into a small room before setting the young penguin down, and then promptly curled up, clearly planning on taking a nap.

Private made a beeline for the open door but stopped dead in his tracks when he saw a penguin walk into the room, closing the door behind her.

"Hello son," she said.

"W-what?" Private stammered. He backed away from the strange female penguin, who apparently was claiming to be his mother. His mother was in England with his uncle Nigel, right? That's what both Skipper and Uncle Nigel had said. Yet, he couldn't help but notice that she spoke with a British accent.

"Look at you," the penguin said, ignoring Private's stammering. She circled around him three times before she stopped in front of him and stepped closer, taking his flippers in hers.

Private could see admiration in her eyes, but he couldn't get over how cold and hateful her eyes seemed to be, even when she was looking at him.

"You look so much your father," she continued, her eyes becoming even colder if possible, "Tell me, how is he?"

Private gawked at her, his eyes wide, "What? Wh-what are you talking about?" he stammered helplessly, while Savio began to snore from his corner of the dark room.

The penguin blinked, and then backed up, frowning now, "Of dear, Private, has he not told you anything?"

Private shook his head, his mind reeling, "I'm afraid I don't understand what you're talking about".

The penguin seemed to feel sympathy for him, for she started explaining a moment later, "Your father, Skipper, he took you away from me when you were just an egg, didn't he tell you that? After all, he seemed to trust the rest of his team to tell them he was a father. Why do you think he put so much effort into raising you?"

"What! Skipper, he-he's not my father! You're lying! If he was, he-he would have told me!" Private yelled, "I don't even know you, why should I listen to you!"

"Because," the penguin said, "I'm your mother Karen". Private gulped, Karen was his mother's name, Skipper and Uncle Nigel had told him so.

"Tell me my boy, does Skipper even care for you. After all, if he was proud of being your father, why wouldn't he tell you what he was to you," Karen continued.

Private scowled, but her words did make sense . . . the feeling of sheer fury began to bubble through the young penguin. Skipper had lied to him, who was to say he hadn't lied about other things . . .

Skipper's P.O.V

The rat army took them to a large casino building, one all too familiar to Skipper. It had been where Slade had first begun to train him and Hans, so many years ago.

Once inside, Skipper saw that it looked very much the way it had then; with the casino machines and tables covered up with white sheets, gathering dust, while training equiptment of every assortment littered the place.

The rats took them to a small area of what had once been the bar area and locked them in a cage behind the wooden bar.

"Good luck getting out of that!" one of the rats chuckled, "especially with Rhonda here to guard you!" and with that said, they walked away, laughing among themselves and high-fiving.

For a while, the group struggled against the cage bars, and Rico tried to unlock the cage door by puking up several useful items, but Rhonda kept swiping them from him until a cold cruel laugh swept through the air, coming towards them. Slow clapping . . .

A shiver ran down Skipper's spine as a dark furred lemur made his presence known in front of them. Deadshot. The very lemur who had turned Skipper into what he was today, and had forced him onto the path of being a commando. The one who had killed his family and his mentor, Slade.

"What have you done with my son?" Skipper demanded, "And how'd you get out of prison?" He shooed his teammates and Julian behind him with his flippers, fully determined to protect them at any cost.

"Oh nothing, he's just meeting his mother for the first time," Deadshot laughed, before he turned his attention to the others behind Skipper, "Tell me lads, do you know who I am?"

"You're an enemy of Skipper's, which makes you an enemy of ours," Kowalski spat, while Rico growled. Even Julian looked furious.

"Let us out of here, I'm the king of lemurs, I demand you too!" the lemur king snarled furiously, coming up to stand beside Skipper; Kowalski and Rico moved to stand next to the older penguin as well.

Deadshot snorted, "Some king," he sneered, and went on to add, "Don't you love my army? Iit wasn't very hard to become their leader, after all they all hate you! And now, we're going to take over New York City, starting with the central park Zoo!" Deadshot cackled, and then left them; leaving Skipper to do nothing more than shout insults at his back.

After a while, the four of them grew tired and huddled in the corner of the cage farthest away from their guard, Rhonda, whispering among themselves, trying to figure a way out.

"After we figure out how to get out of this stupid cage, we'll go find Private, and if Karen hasn't already, then we'll tell him the truth," Skipper said with finality, "Then we go and help the zoo".

"So," Julian drawled, "The Private is your son, but you didn't tell him of this because you were afraid you would not live up to his image of you? Come on, even with you as his leader, he still looks up to you".

"It's a long story Julian," Kowalski muttered, while Rico suddenly stood up, eyes narrowed with anger.

"Hans?" Kowalski snorted, "We should have known you'd be here". Skipper, Julian and Kowalski stood up, and glared at the puffin as he made his way lazily over to Rhonda who looked like she was about to fall asleep. Leave it to the puffin to ruin their plan by making sure their guard didn't fall asleep.

Skipper felt a knife tear at his insides, the last time he had come up against Deadshot, Hans had been on his side, and now it seemed that Hans had switched sides.

"I thought you hated Deadshot," Skipper spat furiously as Hans stopped in front of Rhonda. The puffin wisely chose to ignore him.

"The Deadshot says it's my turn to take a shift as their guard," Hans said, jerking his head at the cage.

"Good," Rhonda yawned and began to move away from the cage, "Cause I'm about to pass out". Hans took her place beside the cage, and while Skipper and Kowalski whispered among themselves on how to take him out, the puffin watched Rhonda until she had disappeared from sight.

Then Hans let out a sigh of relief and started to unlock the cage, his eyes now wide with fear, but determination.

"What are you doing?" Skipper asked icredilous.

"Shush," Hans hissed softly, "They'll hear you!" With a quiet snap, the lock fell off, and Hans pushed the cage door open, "Come on, let's get out of here!"

"Y-you're helping us?" Kowalski's eyes went wide as they scrambled out of the cage. Relief spread through Skipper, Hans it seemed still hated Deadshot as much as Skipper himself did.

"Let's just say I helped put Deadshot into prison last time, and I plan on doing so again," Hans sniffed, and then added to Skipper, "Overheard what you said earlier, went to try and find Private. They're holding him in our old room".

"Old room?" Julian and Kowalski echoed. Skipper's three allies facial expressions all showed confusion, and surprise.

"We had the same mentor who Deadshot later killed; this was our old hideout," Skipper explained, not wanting to go into detail at the moment. He turned to his old nemesis/friend, and said, "Lead the way Hans".


	4. Chapter 4

Chapter Four

There were two rats guarding the door to Skipper and Han's old room, both which were taken out by the latter easily.

"Something's up, there should be more guards," Kowalski said, narrowing his eyes at the door. Looking over at his leader, he could tell Skipper felt the same, and so did Hans.

Kowalski never thought they would be working with him again after the whole Hoboken robot thing, but here they were, working with the crazy puffin.

"Stay alert boys, we're probably be surrounded by hostiles the moment we step foot into the room," Skipper said, raising his flippers in self-defense.

The others quickly copied him, except for Julian, who just walked behind them catiously as they went into the room.

"Private!" Skipper was instantly at the young penguin's side, before he picked him up and hugged him tightly, saying, "You're ok!"

"Yeah, I'm fine," Private huffed. Kowalski did a double take, the youngest member of their team sounded angry.

Skipper seemed to notice too, for he let Private go, and took a step back, examining him, "Private?"

Private folded his flippers across his chest, scowling, "You lied to me! You're my father and you lied to me!"

"How'd you—" Skipper started to say but was caught off when female laughter sounded from behind them.

"You really are pathetic Skipper," Karen sneered, eyes gleaming with savage triumph, "How could you not only steal our son away from me, but lie to him about his parentage as well?"

"What are you talking about?" Kowalski snarled at her, "You abandoned him, Rico and I were there!"

"Private I," Skipper started to say again, but the young penguin cut him off.

"Leave me alone!" Private snapped, clearly hurt, and turned his back on Skipper, "I don't want to talk to you!"

"Sorry to interrupt this family ruining but—" Hans began to say.

"Rat army! Rat army! Rat army!" Julian shouted, jumping up and down, pointing at the rat army approaching them.

That snapped Skipper out of his stammering daze, "Kowalski options," he ordered.

Kowalski swiftly glanced around the room, then upon seeing a window, reported, "Stragetic retreat through the window Skipper,"

"Excellent, go!" Skipper yelled, "Rico kill the window!"

The group bolted for the locked window, which Rico made quick work off thanks to a small grenade he puked up. Within seconds, Kowalski, Rico, Julian and Hans were safely outside. Skipper leapt up onto the ledge, but noticed that Private was still refusing to follow.

"Private, outside, double-time!" he yelled anxiously at his son.

"I don't follow orders from you anymore," Private said softly, his back to Skipper.

"What?" Skipper whispered; feeling tears sting his eyes, "Private please! Let's go home, and I'll explain everything, I promise!"

"My mother already did," Private retorted bitterly.

"Skipper we have to go! We can come back for him later!" Hans, Kowalski and Rico all jumped back up and pulled Skipper out through the window, and onto the ground.

"Head to the zoo!" Skipper rasped, and they all took off as rats began pouring out of the window after them.

 _Ooh! This chapter was so angsty, I hope you guys liked it! Remember, I love hearing what you guys thought of the chapter, so please leave a comment below._


	5. Chapter 5

Chapter Five

Skipper slowly led his allies back to Central Park zoo, his head down, his heart broken by his own son, Private's betrayal.

They were walking silently through New York's Central Park, almost to the zoo, when they saw Marlene and Maurice running towards them, looking anxious.

"What happened?" Marlene demanded when she and Maurice had reached them.

"Your majesty, are you alright?" Maurice asked, skidding to a halt in front of King Julian, who was also rather deflated from their failure of a mission.

"Yeah, I'm fine, but that bad lemur guy!" Julian scowled, "He's no leader!" The lemur king folded his arms across his chest and pouted.

"Skipper what happened?" Marlene asked, taking one of his flippers in her paws. The penguin leader had a far-away look in his eyes, and didn't respond to her, he just closed his eyes and sniffed, attempting not to cry.

Marlene looked to Kowalski for information, "Where's Private?" she asked softly, rubbing Skipper's shoulder comfortingly with her paw.

"H-he chose to side with his mother instead of us," Kowalski rasped, exchanging a worried glance with Rico, both penguins were obviously worried about Skipper, as well as Private, despite his betrayal.

"His mother?" Maurice said, turning to Kowalski, "I thought he would've stayed loyal to Skipper, after all, didn't Skipper raise him".

"Yeah, I did," Skipper said quietly, unhappily, "But I didn't tell him I was his father".

Marlene and Maurice both did a double-take, and stared open mouthed at Skipper, who just stared at his webbed toes as if they were suddenly the most fascinating thing ever.

"Y-you're Private's father?" Marlene said, "And he just abandoned you for the mother he never knew?"

"Animals can do stupid things when they're hurting," Hans reminded Marlene, having not said a word since they left the old casino.

Marlene looked at Hans in surprise, but Kowalski and Skipper quickly explained to her that he hated Deadshot as much as they did, and was now a temporary ally.

"So what do we do now?" Maurice asked, his eyes narrowing in slight anger. He already hated Deadshot just from what the others were telling him.

"We go after this Deadie-shot guy and punch him in the face!" Julian yelped, demonstrating his anger by punching the palm of his left hand, his eyes narrowed in anger.

Skipper looked up at Julian, his sapphire blue eyes beginning to narrow, his facial expression going from unhappy to determined.

This is just like every other time someone turned their back on me, Skipper thought, there's no difference. Private's a grown penguin, he—I can't hurt him! He's my son!

He struggled to blink back tears. He knew deep down he would never hurt Private, even if his life depended on it; but right now the others needed him more. He would have to be strong for their sake.

As the feeling of Marlene resting her paw on his shoulder, Skipper turned his head, and stared into her beautiful brown eyes, feeling a strange sense of calm come over him.

"Don't worry Skipper, Private will see sense soon, and then he'll be back on our side," she told him, offering him a small smile.

Skipper felt his insides turn to goo from the way she was looking at him, and then he smiled shyly at her and nodded, "Thanks Marlene".

He turned back to the others who were waiting for his orders. Skipper shook himself, forcing himself to hide his heartbreak, and told them firmly, "We go at Dawn, and take them down. Then we get my son back".

Sorry I couldn't resist putting Skilene into this story, I've been wanting to do it for a while now. Anyway, hope you liked this chapter.


	6. Chapter 6

Chapter Six

Skipper raised his left flipper, signaling for his allies to halt. It wasn't nearly as many as he had hoped, just his remaining team mates, Hans, Marlene, the chimps, Roy, Darla and her friends, Bada and Bing, Joey, and surprisingly the lemurs.

He had hoped to convince Roger, and Burt, but neither had wanted to fight unless they absolutely had to, and apparently this situation didn't count as absolutely having to.

"You remember what we taught you lot," Skipper called softly over his shoulder to his allies. He, Kowalski, Rico and Hans had taught all the others basic fighting techniques.

"We remember Skipper," Marlene murmured, resting her paw on his shoulder. He felt a smile tugging on his beak, but he ignored the feelings that arose in him.

"Good," he whispered, eyes locked on the very building where he had been raised. It had all started at the consino, and now it seemed that it would end at the casino with Deadshot being captured again.

"Kowalski options," Skipper said, turning to his second in command. Kowalski automaticly pulled out his ever present clip board and began scribbling something down on it, thenpointed with his pencil towards the double wide doors.

"Most likely they have guards posted there and at the other entrances. The bigger animals will have to go through the main entrance, but the rest of us can go through the air vents and take them by surprise. The large animals cause a distraction then we attack and catch them by surprise," Kowalski explained quietly and quickly.

"Alright, gorrillas, chimps, baboons, Joey and Roy will go through the main entrance and act as a distraction, the rest of us will go through the air-vents and take them by surprise," Skipper ordered.

The others nodded in understanding, while King Julian said, "What about the Private? If he is a double agent".

"Leave my son to me Ringtail," Skipper muttered, just loud enough for the others to hear.

Then Skipper and Hans both gave the signal, and the large animals crept towards the main entrance, while the rest of them quickly found the vents located on the side of the building and went up into them.

Soon enough they came to an intersection, and split up so that they would be attacking in two different areas. Skipper led Kowalski, Marlene and Julian, while Hans led Maurice, Mort and Rico.

When they reached the spot that led down into the casino, Skipper halted his group and they waited until they were sure the animals down below were fighting before they jumped down and attacked.

Skipper took out several rats when he landed then with a swipe of his flipper took out a few more, before he lunged to the side to avoid Rhonda's flipper that came crashing down where he'd been just seconds ago.

"Looking for someone Skippy?" Karen hissed, and slammed into him, sending him flying forward and into Rhonda, who moved to squish him, but he quickly leapt out of the way and narrowly avoided another attack from Karen.

"Where's Private?" Skipper snarled, and lunged at her. She easily blocked his flying kick, and leapt onto a table, her flippers raised in defense.

Skipper threw himself at her, and plowed into her.

"Stop!" Skipper froze at the sound of Private yelling. He spun around, eyes wide, but then he felt a heavy blow land on the back of his head from Karen, who seemed like she couldn't care less about if their son saw them fighting.

Private was standing on the other end of the table his eyes wide, "Why are you hurting him mom? He's still my father, and my leader!"

Karen sneered openly at her son, "And why should I care Private? He means no more to me than you do! And soon you'll both be dead for ruining my life!"

Private's eyes were filled with tears and disbelief when Karen lunged at him, ready to kill. Skipper was faster.

He knocked her away from Private and both fell from the table, and once again faced each other, eyes burning in hatred.

Suddenly, Skipper felt thick coils curl around him and then the breath was knocked out of him as Savio began to squeeze him, attempting to kill him, Karen laughed, and then lunged at the now immobile Skipper.

But before Karen could even touch Skipper, Marlene slammed into her, and the two began to wrestle viciously around on the ground.

"Skipper!" Private was suddenly at his side, attacking Savio, along with Kowalski and Rico. Rico would strike at Savio's face, while Kowalski and Private tried to get Skipper out of the massive snake's coils.

The two penguins grabbed each of Skipper's flippers and pulled hard. Finally, he came loose and the four of them tumbled to the floor.

"See you're back on our side Private," Kowalski panted.

"Just because I'm angry doesn't mean I'm a traitor," Private retorted, and together the four of them rejoined the battle.

"Skipper! The otter!" Hans yelled to him from where he was fighting nearby. Skipper spun around in time to see Deadshot throw himself at Marlene, who was still busy fighting against Karen.

"No!" Skipper screamed, and leapt into the way.

He blocked Deadshot's first blows but then was knocked onto his back when the black lemur's tail whipped his feet out from under him.

Deadshot was about to bury his teeth in Skipper's throat, but then King Julian leapt onto the other lemur's back, his eyes blazing with wild fury, "I'm the king of the lemurs, and no one had better forget it!" he yelled.

Hans, Kowalski, Private and Rico were suddenly at their side, and together the six of them took Deadshot down, and knocked him unconscious.

Once the enemy saw that their leader was out cold, they fled quickly, abandoning their leader's original plan.

After that things went quickly.

Skipper and Hans called in Private's uncle Nigel, and he happily took Deadshot away, along with Karen, whom he revealed had tried to kill him because of his job multiply times.

After that, they all went back to the zoo.

By then, it was night, and the penguins made sure to ensure that no human had witnessed their leaving for the day.

Soon Skipper found himself quietly explaining to Private why he had never told him of their blood relation, while the lemurs, the rest of Skipper's team, Hans and Marlene sat nearby, playing a card game.

"When I was young Private, I lived with an eagle named Slade who taught Hans and me about the art of being a commando. Hans ended up betraying us because he was jealous of the extra attention Slade gave me. I didn't tell you I was your father, because I was worried that I would start to do the same thing my mentor had, and that it would tear my team apart. I couldn't let that happen, you can understand that can't you?" Skipper said nervously.

Private nodded and rushed over to Skipper, where he hugged him tightly, "I'm sorry Skipper. I understand".

After a few moments, they went back to the group, and Marlene motioned for Skipper to join her by the edge of the rock.

Skipper sat down beside her, and then they shared a kiss.

Deadshot had haunted him his entire life, but now, his last attempt to take the penguin's life had given Skipper a new beginning, and now he planned to ensure that the ones he cared about, including Hans, who had decided to stay at the zoo with them, would be safe from harm.

The End.

 _This is probably one of the shortest and most intense stories I've written, but I hope you guys liked it._


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